Contacts of the strand formed by residues 640 - 650 (chain D) in PDB entry 2W3S
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASN 640 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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357C PHE* 2.8 26.4 - - - -
457C VAL* 3.9 3.4 - - - -
632D VAL 3.2 14.8 - - - +
633D ILE* 3.8 15.7 - - + -
638D GLY 2.9 20.8 + - - -
639D GLU* 1.3 77.7 - - - +
641D ARG* 1.3 63.3 + - - +
676D THR* 5.1 8.0 - - - +
743D LEU* 4.0 21.2 - - + +
761D ALA 4.5 4.2 + - - +
763D PRO* 4.1 14.5 - - - +
766D VAL* 3.7 16.1 - - - +
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Residues in contact with ARG 641 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268C ARG* 6.1 0.6 - - - +
357C PHE* 4.5 6.7 - - + +
457C VAL* 3.8 20.2 - - + -
458C LEU* 3.4 45.0 + - - +
460C VAL 4.8 7.2 + - - -
631D VAL* 3.3 7.2 - - - +
632D VAL* 3.1 29.4 + - + +
640D ASN* 1.3 81.4 - - - +
642D ILE* 1.3 76.0 + - - +
643D LEU* 3.5 13.5 + - + +
702D SER* 4.6 18.7 + - - +
706D ARG* 3.5 48.8 - - + +
743D LEU* 6.2 0.4 - - - -
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Residues in contact with ILE 642 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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629D THR* 3.9 13.0 - - + -
630D GLU 3.6 2.7 - - - -
631D VAL* 4.2 14.6 - - + -
641D ARG* 1.3 76.7 - - - +
643D LEU* 1.3 63.6 + - - +
644D ARG 4.0 4.0 - - - +
645D THR* 3.6 24.7 - - - +
668D TYR* 4.3 6.5 - - + +
672D ALA* 4.2 24.7 - - + -
676D THR* 5.3 9.6 - - + +
703D ASP 4.5 16.9 + - - +
704D ARG 4.3 2.3 - - - +
705D PRO* 3.8 20.1 - - + +
706D ARG* 3.4 20.1 + - - +
739D ALA* 4.2 11.0 - - + -
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Residues in contact with LEU 643 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460C VAL* 3.8 18.6 - - + +
462C PRO* 3.4 41.7 - - + +
446D ARG* 3.9 27.1 - - - +
630D GLU* 2.7 27.6 + - + +
631D VAL 4.2 5.2 - - - +
632D VAL* 3.4 35.7 - - + -
641D ARG* 3.5 13.8 + - - -
642D ILE* 1.3 73.5 - - - +
644D ARG* 1.3 60.4 + - - +
706D ARG* 3.1 11.9 - - + +
707D ILE 3.1 21.7 + - - -
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Residues in contact with ARG 644 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462C PRO 5.2 3.4 - - - -
424D SER 4.8 2.4 + - - -
425D ALA* 3.7 18.6 + - - +
426D ASN* 5.6 1.4 - - - +
430D ARG* 3.4 37.0 + - - +
628D ILE 3.7 1.1 - - - +
629D THR* 3.3 3.1 - - - +
630D GLU* 2.7 41.9 + - + +
642D ILE* 3.5 2.5 - - - +
643D LEU* 1.3 82.5 - - + +
645D THR* 1.3 66.2 + - - +
646D ASP* 2.8 37.1 + - - +
705D PRO* 4.6 0.7 - - - -
707D ILE* 3.3 42.4 - - + +
709D ASN* 4.0 7.8 - - - +
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Residues in contact with THR 645 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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627D ALA* 4.6 1.1 - - + -
628D ILE 3.2 10.3 - - - +
629D THR* 3.5 1.6 + - - +
642D ILE* 3.6 3.5 - - - +
644D ARG* 1.3 77.7 + - - +
646D ASP* 1.3 69.7 + - - +
647D ILE* 3.8 21.5 - - + -
668D TYR* 2.7 52.0 + - + +
705D PRO* 3.4 18.2 - - - +
707D ILE 2.9 10.3 + - - +
708D PHE* 4.2 4.0 - - + -
709D ASN 2.9 24.6 + - - -
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Residues in contact with ASP 646 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421D LEU* 3.7 12.1 - - + +
425D ALA* 3.8 21.0 - - + +
430D ARG* 2.7 30.2 + - - +
627D ALA* 3.3 3.1 - - - -
628D ILE* 2.9 35.6 + - + +
644D ARG* 2.8 24.9 + - - +
645D THR* 1.3 73.3 - - - +
647D ILE* 1.3 61.4 + - - +
709D ASN* 2.9 35.6 + - + +
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Residues in contact with ILE 647 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421D LEU* 4.2 3.5 - - - +
626D ALA 3.4 7.9 - - - +
627D ALA* 3.6 18.2 - - + -
645D THR* 3.8 9.4 - - + -
646D ASP* 1.3 75.3 - - - +
648D LEU* 1.3 66.5 + - - +
649D HIS* 3.9 5.4 - - + -
664D ILE* 3.9 19.5 - - + -
668D TYR* 3.8 30.5 - - + -
708D PHE* 3.9 14.1 - - + -
709D ASN 2.7 12.9 + - - +
710D VAL* 3.4 7.1 - - + -
711D ALA* 2.6 34.8 + - - +
735D LEU* 3.5 31.9 - - + -
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Residues in contact with LEU 648 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417D LEU* 3.6 42.8 - - + +
420D ARG* 3.9 22.0 - - + -
421D LEU* 3.9 22.1 - - + +
424D SER* 5.9 0.4 - - - +
625D GLY* 3.5 2.4 - - - -
626D ALA 2.9 30.2 + - - +
647D ILE* 1.3 73.5 - - - +
649D HIS* 1.3 59.4 + - - +
711D ALA* 3.2 29.2 - - + +
712D LEU 3.7 17.3 - - - +
713D TRP* 3.7 18.2 - - + +
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Residues in contact with HIS 649 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417D LEU* 4.8 0.2 - - - -
453D VAL* 5.1 3.6 - - + -
623D ALA* 5.1 0.6 - - - +
624D TYR 3.4 19.1 + - - -
625D GLY* 3.5 10.0 - - - -
647D ILE* 3.9 11.2 - - + -
648D LEU* 1.3 75.9 - - - +
650D ASP* 1.3 82.2 + - - +
651D ALA* 3.7 1.8 + - - -
664D ILE* 3.6 33.2 - - + -
711D ALA 2.8 9.8 + - - +
712D LEU* 3.2 8.5 - - - +
713D TRP* 2.6 31.8 + - - -
728D VAL* 4.2 9.4 - - + +
731D PRO* 3.9 27.6 - - + +
732D PRO* 3.7 24.6 - - + +
735D LEU* 4.2 12.7 - - + +
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Residues in contact with ASP 650 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413D VAL* 4.7 2.4 - - + +
417D LEU* 4.5 2.9 - - + +
623D ALA* 4.4 7.4 - - - +
624D TYR* 3.0 40.2 + - + +
625D GLY* 4.3 0.4 - - - -
649D HIS* 1.3 86.1 + - - +
651D ALA* 1.3 58.7 + - - +
652D GLY* 2.8 30.1 + - - -
713D TRP* 3.7 33.1 - - + +
715D GLN 4.3 1.9 - - - +
726D LYS* 2.5 40.8 + - - +
727D ALA 4.5 1.9 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il